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Escape curly bracket in regex which fails for new perl versions

escape curly bracket in regex which fails for new perl version

Chromosome mappings updated so species is at a separate level from ucsc_to_ensembl and ensembl_to_ucsc entries

- Add a MeTooDelete callback module that looks backwards if a record has been deleted, and deletes the current record if so
- Update the gff3_filter_large example to use MeTooDelete to full clean a GTF/GFF3 record set for large records

Callback processor to rewrite fasta headers, given a fasta header format regex string and the lookup tables to use for substitution

A soft error if an attribute in the configuration file doesn't exist in the gxf file being processed.

Will likely only work GTF<->GFF3, metadata may not be formatted correctly, and if other format conversions are attempted it will likely explode spectacularly.

- Created a GTF parser to enable properly parsing metadata in this format

- Added transcript_id filter to mirror gene_id to transcript_id in gene records to make tools such as RNA-SeqC happy with our GTF format
- Updated GTF processor to properly format GTF on write with proper delimiters for attributes field
- Removed some debugging output left in FileHandle object
- Fixed issue where parser object type was being overwritten on the actual parsing of a file

- Update copyright year

- Remapping module and example

- Metadata is treated like an object for processing
- Look-back buffer for the previous written record and the previous processed record

- Added a filter callback to do matching, regex and equalities on fields in a record to include or delete that record from the output

- Created first real filter, to remove padding from sequence type objects
- Base configurations for unpadding filter

- Documentation on config format and example config and command lines

- Don't buffer the output when writing
- Dummy callbacks should chatter their debugging data to STDERR rather than STDOUT

Turn on coveralls